AFNI Message Board

Dear AFNI users-

We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:

https://discuss.afni.nimh.nih.gov

Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.

The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.

Sincerely, AFNI HQ

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Karelo
December 17, 2019 12:01PM
Dear AFNI experts,

We realized that we have voxels outsite of the brain with very low values (e.i. 0.0867) after we run: 

3dAllineate -prefix output.nii -base MNI_template -source Image -1Dmatrix_save file_aff12.1D


Then, after using 3dQwarp, these low values extend even further. We run the command in the following way: 

3dQwarp -prefix output_Qwarp.nii -base  MNI_template -source  output_allineate.nii  -nmi  -workhard


Please see the attached images. We would like to know if these steps are correct. If so, should we do something the erode the low values? or is this normal?

Thanks in advance,
Karel
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Attachments:
open | download - allienate.jpg (17.1 KB)
open | download - Qwarp.jpg (18.9 KB)
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Subject Author Posted

Possible problem with 3dAllienate and 3dQwarp Attachments

Karelo December 17, 2019 12:01PM

Re: Possible problem with 3dAllienate and 3dQwarp

ptaylor December 17, 2019 01:58PM

Re: Possible problem with 3dAllienate and 3dQwarp

Daniel Glen December 17, 2019 04:38PM

Re: Possible problem with 3dAllienate and 3dQwarp

ptaylor December 18, 2019 12:19AM